A scientist's revenge
by thefifithpenguinofmadagascar
Summary: Kowalski has always been different, his intellect proving invaluable. But what if he begins to see the zoo for what it really is: a freak show for humans to look at. With Skipper unable to understand he turns to a kindred spirit, one that will understand and has crossed blades with Skipper and his team before... Follow the team as they operate trying to get Kowalski back on side.
1. The sign

**A scientist's revenge**

**Hi guys, this is my first Fanfiction so be nice please and review it. It has been beta'd by my fave author Claws2501 who writes things for Waterloo Road and Star Wars, please visit it have a look at the stories they are amazing!**

**So, essentially the story will be about Kowalski and the team, and how the team operate without their favourite brains around. Its going to be fun, and dangerous and...did I happen to mention dangerous. Bit is a Kowalski whump but hopefully its going to be ok.**

**Legal jargon: I do not, and will ever not own Penguins of Madagascar. It belongs to DreamWorks and Nickelodeon. Unless I win a huge lottery sum this will never change. However, you will notice some OC's they are mine and I own those.**

**Please enjoy and review**

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"Everyone topside at 0800 hours for training" Skipper called out, watching his unit arouse themselves. It was just two weeks after the Chuck Charles mission, and things were beginning to settle back into some sort of routine, helped no end by his second in command and faithful friend: Kowlski. Naturally, the group still had to deal with the antics of 'king' Julian and his lemur troupe but on the whole, things were relatively quiet. He turned to his right shoulder naturally, it was funny, everything about this group seemed natural now, familiar even, and his life on the rough was a long long way away from this.

"Kowlski, give me a run down of today's schedule" again, a natural, well-worn phrase between commander and lieutenant, but also between trusted friends. When the answer was not forth coming he turned further around. "Kowlski" the penguin repeated, "give me today's schedule" this seemed to shake his friend out of wherever he had been.

"Sorry Skipper, my cortex was…" Skipper cut him off.

"What's the schedule?" he repeated.

"Training at 0800 followed by you going to see Marlene at 0830 and then the rest of the day we have a school trip so good practice for the 'cute and cuddly' routine" Kowlski reeled off and Skipper smiled slightly in satisfaction, every penguin had their off days he thought.

"Right then, training" the leader said before hopping off and climbing upstairs to their habitat's platform. The rest of the team followed, albeit Kowlski a little slower than the others still pondering and deep thinking as he does, but this was useal and went largely unnoticed by the team.

When they got topside all four penguins were greeted by a shock: a large board obstructed their vision into the zoo, now, if they wanted to do an local recon they would have to jump onto their railings and over the other side. They stared at in dumbfounded, patiently waiting for Skipper's order to quickly go and have a closer look at whatever it was.

"Kowlski…give me options," Skipper said as he and the rest of the team stared at the sign.

"Well…it appears to be some kind of sign for the humans" the lieutenant started getting cut off by Skipper.

"Tell me something I don't know" his leader explained prompting Kowlski to curl his fin up slightly, berating himself for not being able to, for once, appease the leader. "It's…" he began, anger colouring his voice ignoring the way that all his other comrades stared at him slightly. "I don't know Skipper," he admitted slightly.

"You don't know" Skipper gasped, his flippers went straight to his head and his beak opened in shock. "How can you not know?" he asked wearily.

"Well skipper, it appears to be some kind of message about feeding times but there are too many symbols for just feeding, there is something else going on" Kowlski looked around nervously, as if something were to come out of the very bushes they were standing in front of. "We need to get the chimps to interpret this message for us immediately".

"Best get some fruit then" Private piped up already waddling towards the lemur habitat with Rico.

The lemur habitat

Rico and Private leapt over the wall to the lemur enclosure. Slithering on their bellies they crawled underneath a tree to do a quick recon of the area, it was natural to them, danger could be lurking behind every corner and these penguins were not going to let themselves get fooled by the apparent safety of the zoo. A tail swept across the penguin's vision and they cuddled closer together, holding their breath to become, as Skipper would say: 'silent at the grave'. It would have worked, however following the tail was by a tiny cuddly rat-like creature that quickly alerted the owner of the tail to the presence of the penguins. Private and Rico shared a look, it was true: they were used to 'King' Julian's antics but it wasted time, time which they didn't know they had.

"Your king, that's me, demands you to get out of his kingdom with immediate effect" Julian proclaimed making a sweeping movement with his hands to demonstrate them leaving. The penguins shared a look, before turning back to Julian who was still looking around trying to find them. Really, he wasn't the brightest; Private decided to take the plunge and waddled out to meet him, Rico followed quickly behind him. "Maurice" Julian called, "deal with them". Maurice looked towards them awkwardly.

"His Majesty still believes that your antics the other day caused the sky gods to be royally angered". Again Private and Rico shared a look, it was brief, but for the way these penguins worked it was all that was needed.

"That's the thing" Private began, feeling rather than seeing his comrade actively nodding beside him. "We want to help with the sacrifice". He felt three pairs of eyes on him and shrank back slightly into Rico's bigger and far more scarier form, he wasn't scared, Dr. Blowhole was scarier than this, but he knew that it made his appeal seem more realistic. He had watched Skipper too many times to not know how to be a little sly, and his time in London had leant itself to this task. "Skipper says that the sky gods made contact with him in the night and have demanded a sacrifice". Julian stiffened his eyes widening slightly.

"The gods made a demand to Skipper?" Private inwardly cringed, he had forgotten the big lesson: appeal to ego. Rico behind him was tensing; he to had sensed the mistake.

"What we mean is, Skipper had been requested, no demanded, to take some of the sacrifice you are offering and use it to offer to the sky gods" he paused trying to gauge the reaction of lemur. Rico behind him was also holding his breath.

"Does that mean…" Julian asked trying to process and be ahead of the penguins but unable to keep up with the bird's brains.

"It means" Private said, deciding to help out. "It means that the sky gods have decided you have made enough sacrifice and technically you haven't done anything wrong, we are the culprits the sky gods need us to sacrifice things instead" Private's eyes shone with sincerity and it made Julian just want to believe him and a few minutes later a huge bowl of fruit was being pushed towards the penguins.

"Take it, as a donation from your most gracious king, that's me, and please fulfil your punishment". The penguins quickly pushed the bowl away and once they were safely out of the habitat they began laughing gleefully unable to hide their happiness at having learnt from Skipper's hardest lessons.

Penguin HQ

"Just smile and wave Kowalski, smile and wave" Skipper exclaimed waving his flipper to and fro trying his best to ditch his commando façade and try his cutest smile. He wouldn't admit it to anyone else but one of the reasons he saw Marlene was to practice, away from his colleagues. To him, not being able to practice what he preached showed weakness and Skipper never showed weakness, ever. But still, be believed whole-heartedly in the routine. It have them extra food after all, but today, his second in command was just not on form today, it was obvious because right now Skipper was getting more food.

"Argh" Kowalski groaned, he looked down dejectedly as he heard something spoken by one of the younger pups. Skipper could see the point, yes the did pull faces, and yes they also had a few bits of rubbish strewn around the habitat, but again, it was their place, they were birds. It was their job just like it was their job to protect the zoo. Any other thinking would be nothing short of what the dolphin Blowhole thought, and that WAS unacceptable. Kowalski turned around towards Skipper, aware that he was both being watched and being studied and opened his mouth to speak.

"We got the fruit Skipper," said a voice directly behind Kowalski, causing Skipper to raise his non-existent eyebrow. Then he noticed Private, previously obscured by the sign around their enclosure.

"Well you guys are tardy to the party aren't you?" Skipper asked pushing his thoughts for his second in command aside, he can deal with him later. His eyes widened as took in the huge bowl that Rico was carrying above his head.

"We did it Skipper" Private exclaimed, his eyes shining from a job well done and he looked expectantly up at Skipper waiting for praise. Skipper looked him up and down.

"And a job well done Private" he said, it wasn't cause and effect praise, and everyone knew that Skipper's praise was rarely given and highly sought for. His team knew when and how to please him and that was not ever a bad thing.

"We better get going" the second in commands voice rang out, but it sounded wrong, almost bitter far from the distant self that their scientist friend was. Rico and Private turned to Skipper questions forming in their beaks but they were shot down quickly.

"How right you are," Skipper agreed before making his way towards the edge of his habitat, already being replaced his hologram self from the underground base's projector. No was he going to explain himself to his team. Yet. But they had noticed the change too and for Skipper that was really worrying because for once he wasn't being paranoid. He felt the other three flip and slide towards him as they made their way across the zoo.

Chimp enclosure

"Ahh yess your gratuity is accepted" Mason's drawl rang out across the enclosure. Skipper slapped his left flipper to his face, they had covered this aspect already and yet the monkeys, for that's what they really were in the penguins mind, still insisted on these huge theatricals every time someone tried to make a dealing with them. It was hard for Skipper to work with them, he didn't trust anything that wasn't black and white and these monkey's were somewhere in the middle.

"How many times to I have to tell you, it's a B-R-I-B-E" he said exasperatingly, the need for information and being forced to rely on these human-brained idiots was making his fuse shorter than it normally was. He watched as they salivated over the bowl of fruity goodness. Kowalski stepped forward with the sign and his movements told Skipper he too was having a tough time controlling his temper towards them. This was strange, but not unusual so Skipper decided to ignore it.

"Can you interpret this sign?" he said pointing towards their own habitat and the huge sign wrapped around the railings. Phil moved towards the edge of his cage, fishing out some opera glasses so as to better see the symbols and nodded at Mason, signalling he understood the sign. The first chimp then turned to the penguins and did a serious of bizarre hand movements that was the only way he appeared to be able to respond to direct questions. They waited patiently for Phil to translate when Private burst out with happiness.

"He's here?" The little penguin asked, causing all of them to turn and look at him questioningly

"Private" Kowalski began and was cut off by Skipper.

"Who is here?" he asked looking around, his paranoia kicking in. He tried to breath and force it back down he was not going to loose it in front of him team. He hadn't before, and he will not be doing it now.

"My keeper from London, oh he was so nice, I do hope he remembers me" Private exclaimed. Now it was time for the Chimps to get grounding in the conversation.

"Pardon me my friend" Mason spoke up, his colleague signing behind him "how did you understand I had not even begun to…" He stopped as he stared at Private who looked down almost ashamed, he had forgotten to tell Skipper, wanting just one secret to himself he had decided that he would keep quiet about the ability to understand British Sign Language, something he had picked up from being the favourite amongst the group to the zoo keeper in ZSL London.

"I can read BSL," he said before quickly explaining. He looked up, peeking a look at Skipper, and looked down again unable to meet the eye of his leader and comrade. Finally the leader spoke.

"We better get back to our own enclosure" he said finally, "And you" he stressed 'you' at Private. "Better tell us a little bit more than 'he's here'". Private looked down dejectedly, he was in the doghouse and he just hoped he would survive the court martial to come.

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**Soooo...What did you think please review at let me know :) **

**thefifthpenguinofmadagascar **


	2. The realisation

**A scientist's revenge: chapter 2**

**Hi,**

**Thanks for the reviews:**

**Alexia1012- thanks for the welcome and glad your enjoying the story**

**611-L- Thanks for the following, and glad your loving it. Kowalski is getting there, tell me was this what you were expecting?**

**hmbird11- wording noted, thanks for reviewing, is this any better?**

**New readers and old welcome to chapter two, enjoy:**

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Dinnertime was a special time for the penguins, a time when tactics were bantered about and stories shared about happy moments during the day. It was a time when the deception that they held around them all day would be shed, no secrets in the base: everyone knew who everyone else was. However, it was equally a time to question teammates on matters, which didn't need further action such as court martial.

"So Private…" Skipper began, he normally would be the first to start a questioning, and he was leader: he needed to know.

"Yes Skipper" Private chirped out, he seemed happier somehow, as if a great weight had been lifted. He wasn't cowering like normal under Skipper's questioning gaze.

"How could you interpret what the chimp was saying before his apey friend did?". Private looked around the table meeting each questioning gaze in turn before looking down at his day's worth of fish and back up again.

"I learnt it in London!" Private exclaimed almost straight away wanting to defend himself, it wasn't that he wasn't happy with the team not knowing; it was the way they wanted to know. He wasn't a criminal.

"Fascinating" muttered Kowalski, his mind clearly halved between the conversation and some distant thought.

"Its true!" Private squeaked, his voice going up several octaves with volume. "I was there when the Paralympics was on…its to help people who can't hear!"

"Thank you Private" Skipper said already turning to a different conversation, he thought as such, and when one of his team confirmed what he already knew he didn't need any other persuasion.

"Skipper..." Private started trying to get his own back on the Spanish Inquisition.

"Yes Private?" Skipper said, raising a non-existent eyebrow.

"A…Secret…for a erm…secret?" Private asked nervously rubbing his fins together to try and comfort himself.

"What does that mean Private?" Skipper asked perplexed by the sudden change in conversation.

"Well…I" he was interrupted by Kowalski.

"I believe he means one of us now needs to say something about ourselves" he muttered not even bothering to look up at his leader. Skipper frowned and turned back to Private who positively cowered under his gaze.

"Well what do you want to know Private?" he asked bending over the table, hand on his flipper. To a spectator he would seem totally at ease with the conversation, but inside he was a penguin balancing on a knife-edge. It was a direct challenge against the demons of his past, a challenge he was not yet ready to face.

"Erm…Well..Skipper…The thing is…er…Denmark" Private squeaks and covers his beak as if he had uttered something disgusting and dirty.

"I told you Private that is specifically between me and the Danes" Skipper murmured, his confidence petering out as he was forced internally to admit he could not yet face the demons of his past.

Recon- 2000

With the zoo divided into 5 different sections the penguins split: jumping over the small iron wrought fence posing no threat or barrier to them.

"Alright split up, you know the drill" Skipper commanded, total confidence in his time allowing him to keep walking away from his team to his own mission.

Kowalski too turned the other way, but for a different reason. Military protocol always stated to never turn your back on a leader, and yet, this was exactly what the lieutenant did to his commander. An action that was not lost on Skipper who frowned slightly, but kept walking, he would deal with it later he decided.

Kowalski was spitting sparks, almost literally, except his own brain didn't allow him to think in metaphors like that. It was impossible to spit sparks, unless you were Rico. He had been thinking a lot in the past week, and as he crept stealthily around the zoo it became even clearer how wrong Skipper was about the life they led. They weren't commandos anymore, they used to be and Kowalski missed the time spent in Madagascar, Europe, Africa…That was living. He pushed into the Reptile house, cringing at the fake humidity of the hut; it truly was horrible- the wrong environment for a penguin.

"Come in Kowalski" Skipper's voice rang over the communicator device they used. Sighing internally Kowalski drew a shield of calm around him and proceeded to answer.

"All's quiet in the reptile house Skipper, everyone's a sleep, over" he turned once around on the spot taking in the scene: the harsh fluorescent lighting, the rubbish scattered around the hard concrete corridor that the young penguin stood in. Hard and cold like ice, and suddenly a yearning filled his heart, a yearning to visit the place he should be, to be with the penguins that nature dictated, in the environment that nature wanted him to be in. He growled to himself, and clenching and unclenching a flipper he proceeded to walk out the doors swinging shut behind him, but not before swinging outwards. The door hit him, sending the young penguin flying into some metal chicken wire, his head sticking in between the wire and staying there.

Kowalski struggled for a moment angrily cursing everything from Skipper to the Danes and back again. He sagged for a moment thinking about all the injustice of the zoo.

"Kowalski come in" Skipper's voice came again; this time even the scientist could not miss the concern that coloured his voice. Kowalski struggled again but this time, without the anger clouding his reasoning he quickly freed himself. Bouncing on the pavement he looked up at the wire fencing around the enclosure.

"Kowalski" Skipper said again, his voice turning from mild to strong concern, and another emotion that the penguin commando couldn't quite detect. Was it possible his leader was scared…for..him?

"Skipper, I'm here" he said, his rush to please his leader making him forget standard protocol, something that didn't go unmissed by Skipper.

"Protocol Lieutenant" he said sharply, making Kowalski convince himself that he had imagined the fear before. "Where are you" Skipper asked distracting from his original message.

"I'm…" he looked around and up to the statue which all penguins didn't want to see. "I'm" he repeated unable to get the words out as images flooded him of his past, outside of the zoo with his friends, him his friends, the wild. It had been beautiful. This he thought angrily, looking around the large fenced pen that was build for Alex, the lion who ran away to the circus. Alex, who was with his friends right then: living the dream, maybe not the dream that Kowalski wanted, but their dream.

"Doris" he whispered, his voice reverberating around the empty pen. Doris, the love of his life who was out there that moment living, as she should, free, a true daughter of the waves. No human would tie her down, no human had the right to bind her and lock her in a tank. A tank like some of his comrades was in right then. Nothing would be more fitting, and he should be with her, swimming and flipping and spiralling with her. Dancing, as they should, two halves of the same whole. Instead…instead he was in concrete, bound, Doris would be ashamed of him. With the thought of his love, his dolphin, his thoughts journeyed to another dolphin. One that was right now not thinking to dissimilarly to him, he whispered the name, the word rebounding around the empty concrete enclosure, mocking him and teasing at the same time. One word. Blowhole.

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**Thanks**

**Fifthpenguinofmadacasgar**


	3. let sleeping penguins lie

**A Scientist's Revenge**

**only a small chapter this time...more or less a filler... but an essential one**

**reviewed by claws2501**

**enjoy**

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Inside penguin HQ

Rest and Recreation was now in progress. Rico was playing cards with Private, who was getting repeatedly distracted by the TV blaring out The Lunacorns. Skipper was painstakingly updating his log, something that he felt needed to be done but despised the way it took time away from his team. The only one of the family away from the room was Kowalski, down in his lab with a few of Chuck Charles's reports for accompany. Skipper glanced around worried about it, everyone had heard the second in command's outbursts over the past weeks, the lack of protocol, the unwillingness to participate in some exercises, watching documentaries as if they were cute romantic chick-flicks. Something had to be done, tonight.

"Private" Skipper spoke and instantly he had the attention of Rico too, it only highlighted more to the leader the difference of their final tem member. Both of them were concerned.

"Go" Private, said already turning back to the TV laying down a card flippantly, Rico nodding and making noises in time to Private's speech. Skipper nodded glad at how much of a unit the team was thinking like now. He turned into the lab.

Kowalski's Lab

Skipper pushed into the lab, standing at the edge, hovering and waiting to be acknowledged by the other occupant. He was fully aware that down here he wasn't the leader, and he respected that.

"Newton's knickers, Skipper can you not knock? I was busy" Kowalski exclaimed, quickly shoving a map with flashing dots around it behind a bookcase. Skipper huddled down beside the door waiting for the penguin to stop hiding things away. Skipper took the moments to reflect on what could be wrong and he came up with two scenarios, both leading to one emotion: jealousy.

"You're jealous" Skipper stated.

"I shall not dignify that response with an answer." Kowalski replied instantly then paused fiddling with the corner of what Skipper knew was a map he had been mere seconds before engrossed in. "erm… maybe…yes you could say I was jealous" he muttered. Skipper sighed, the fact his team member had at least admitted this permitted him to safely enter the lab and settle himself down on a seat opposite the troubled Kowalski.

"Look…Kowalski…" Skipper said resigning himself to giving the scientist, who was so factual, so…unemotional… a talk about sharing feelings and people. He really was like an over attached girlfriend sometimes.

"Look…Skipper" Kowalski replied sighing twisting and fidgeting in his chair.

"Me and Marlene…we are...I…" Skipper struggled to grasp his feelings of the otter trying to work out how to begin to describe his feelings for the female otter.

"I don't care" Kowalski exclaimed suddenly and venomously. There was so much feeling behind it that Skipper rocked backwards as if struck by an invisible force. He breathed in for a long moment as if he was trying to drain the oxygen from the lab. "I'm sorry," he said again finally. "I don't care," he repeated in a much calmer state. "You and Marlene… You two are an item, you're beautiful together". He paused to look at Skipper. "You want to be together I am not getting in the way of that". He looked like he'd calmed down a little bit so Skipper pressed to find out what was wrong.

"Just… Kowalski…Please…" In return to Skipper's pleading Kowalski gave him a look close to pure loathing.

"I can't take this anymore!" He exclaimed sending Skipper's mind reeling, but Kowalski was just heating up, and, like an untended pressure cooker he exploded. "Look at Alex, Melman, Gloria and Marty, they are free to do what they like! Doris, she can swim from continent to continent without being tied down" he paused his eyes growing misty at the mention of the dolphin's name. "It would be a crime to cage her". He shook his head to clear his mind. Skipper cut into the ranting.

"At ease solider" He commanded. "You have the right to speak your mind but not the right to get angry" he paused, inside he was in chaos, he couldn't deny that it he hadn't thought what the lieutenant was thinking, every zoo animal had, at least once. However, this was different, what Kowalski was thinking was not: yes this is bad but I couldn't survive in the wild. Instead, he was being driven by love of his dolphin or hate for the humans or maybe both, even more troubling was, out of all the animals in the zoo Kowalski, the brilliant scientist, had the skill and nerve to do something about it. The situation needed to be defused.

"Leave Kowalski" The two words were out of his beak before he had registered them or had time to stop them. "Kowalski" he said again quietly unsure where to now take the conversation. True, leaving would help, but it wasn't originally what Skipper wanted, but having said them he would appear a pretty weak leader to go back on it. He steeled himself for what the newly out casted penguin would do next.

"Science is on my side Skipper" he says slowly clearly still trying to register what had just happened. Tears welled up in the penguin's eyes as he headed for the back door, not wanting a scene in front of his two friends, especially Private. Skipper remained silent trying to find a way to undermine Kowalski's words, to put himself back in control. Nothing game to mind.

"Kowalski" he said again quietly.

"No Skipper" Kowalski replied harshly. "My only regret is that you cannot begin to understand what I've discovered.

He was gone before Skipper could finish blinking.

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**dun dun daaaaaaaaa so kowalski has left...**

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**the fifthpenguinofmadagascar**


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